This function calls
salmon
using system2(). To run in parallel, register a parallel backend, e.g.,
using doParallel::registerDoParallel().
Usage
salmon(
filepaths,
samples,
indexDir,
outputDir = "salmon_output",
cmd = "salmon",
args = c("-l A -q --seqBias --gcBias --no-version-check -p",
foreach::getDoParWorkers()),
compress = TRUE
)Arguments
- filepaths
Paths to fastq files. For single-end reads, each element should be a single filepath. For paired-end reads, each element should be two filepaths separated by ";".
- samples
Corresponding sample names for fastq files.
- indexDir
Directory that contains salmon index.
- outputDir
Directory in which to store output. Will be created if it doesn't exist.
- cmd
Name or path of the command-line interface.
- args
Additional arguments to pass to the command-line interface.
- compress
Logical indicating whether to gzip the quantification file (quant.sf) from salmon. Does not affect downstream analysis.